{
  "abstract": "The concept of a core microbiome emerged from host‐associated research to describe microbial members or functions conserved across clearly defined spatial, temporal, and biological boundaries. In soil‐ and plant‐associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study‐specific thresholds or criteria. Synthesizing recent literature and cross‐site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset‐specific analytical criteria. Taxa designated as ‘core’ were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic ‘core’ members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, ‘core microbiome’ should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as ‘explanatory subsets of taxa’. Greater terminological precision will improve cross‐study comparability and strengthen ecological inference in plant–soil microbiome research.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Agricultural and Biosystems Engineering Iowa State University Ames IA 50011 USA",
    "DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois Urbana‐Champaign Urbana IL 61801 USA",
    "The Great Lakes Bioenergy Research Center University of Wisconsin‐Madison Madison WI 53726 USA",
    "Department of Bacteriology University of Wisconsin‐Madison Madison WI 53706 USA",
    "Department of Plant and Agroecosystem Sciences University of Wisconsin‐Madison Madison WI 53706 USA",
    "Department of Plant, Soil and Microbial Sciences Michigan State University East Lansing MI 48824 USA",
    "Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA",
    "The Center for Bioenergy Innovation Oak Ridge TN 37831 USA",
    "Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA",
    "Joint BioEnergy Institute Berkeley CA 94608 USA",
    "Carl R. Woese Institute for Genomic Biology University of Illinois Urbana‐Champaign Urbana IL 61801 USA",
    "Department of Integrative Biology Michigan State University East Lansing MI 48824 USA",
    "Department of Microbiology, Genetics, and Immunology Michigan State University East Lansing MI 48824 USA",
    "Department of Genetics University of Georgia Athens GA 30602 USA",
    "Department of Chemical Engineering The Pennsylvania State University University Park PA 16802 USA",
    "Plant Resilience Institute Michigan State University East Lansing MI 48824 USA"
  ],
  "article_type": "article commentary",
  "arxiv": null,
  "author_total": 23,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Jaejin Lee",
      "orcid": "0000-0002-9793-9473"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Bolívar Aponte Rolón",
      "orcid": "0000-0002-2544-4551"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Phillip de Lorimier",
      "orcid": "0009-0000-3543-9644"
    },
    {
      "affs": [
        2,
        3,
        4
      ],
      "name": "Jean‐Michel Ané",
      "orcid": "0000-0002-3128-9439"
    },
    {
      "affs": [
        2,
        5
      ],
      "name": "Gian Maria Niccolò Benucci",
      "orcid": "0000-0003-1589-947X"
    },
    {
      "affs": [
        6,
        7
      ],
      "name": "Alyssa A. Carrell",
      "orcid": "0000-0003-1142-4709"
    },
    {
      "affs": [
        8,
        9
      ],
      "name": "Yen Ning Chai",
      "orcid": "0000-0002-2437-9524"
    },
    {
      "affs": [
        1,
        10
      ],
      "name": "Janith Chandrasoma",
      "orcid": "0000-0002-6357-500X"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Nicole Geerdes",
      "orcid": "0009-0001-5904-9533"
    },
    {
      "affs": [
        2,
        4
      ],
      "name": "Valentina Infante",
      "orcid": "0009-0009-6705-1754"
    },
    {
      "affs": [
        2,
        11
      ],
      "name": "Brandon Kristy",
      "orcid": "0000-0003-2421-7143"
    },
    {
      "affs": [
        6,
        7
      ],
      "name": "Stanton Martin"
    },
    {
      "affs": [
        2,
        12
      ],
      "name": "Imani Pascoe",
      "orcid": "0000-0001-8784-3542"
    },
    {
      "affs": [
        1,
        10
      ],
      "name": "Rounak Patra",
      "orcid": "0000-0002-5822-466X"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Lorien Radmer",
      "orcid": "0000-0003-2500-5062"
    },
    {
      "affs": [
        6,
        7
      ],
      "name": "Tomás Allen Rush",
      "orcid": "0000-0002-3207-1466"
    },
    {
      "affs": [
        7,
        13
      ],
      "name": "Ndenum Suzzy Shita",
      "orcid": "0000-0002-8532-7146"
    },
    {
      "affs": [
        1,
        10
      ],
      "name": "Andie Suratt",
      "orcid": "0000-0002-7768-3693"
    },
    {
      "affs": [
        1,
        7,
        14
      ],
      "name": "Patrick F. Suthers",
      "orcid": "0000-0002-5560-9986"
    },
    {
      "affs": [
        6,
        7
      ],
      "name": "Melissa A. Cregger",
      "orcid": "0000-0001-8329-366X"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Adina Howe",
      "orcid": "0000-0002-7705-343X"
    },
    {
      "affs": [
        2,
        5,
        12,
        15
      ],
      "name": "Sarah Lebeis",
      "orcid": "0000-0001-9417-9678"
    },
    {
      "affs": [
        8,
        9
      ],
      "name": "Henrik Vibe Scheller",
      "orcid": "0000-0002-6702-3560"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/112xsg20nfc2c.bib",
  "cited_by": 1,
  "doi": "10.1111/nph.71509",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13738671/",
  "id": "112xsg20nfc2c",
  "issns": [
    "0028-646X",
    "1469-8137"
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  "landing_url": "https://doi.org/10.1111/nph.71509",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Forum"
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    [
      "heading",
      "Viewpoint"
    ],
    [
      "openalex",
      "2303|Microbial Community Ecology and Physiology"
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  "openalex": "W7203650741",
  "pdf_url": null,
  "pmcid": "PMC13738671",
  "pmid": "42608078",
  "published": "2026-08-17",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/112xsg20nfc2c.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T12:23:37Z",
      "native_id": "PMC13738671",
      "source": "pmc",
      "url": "https://doi.org/10.1111/nph.71509"
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  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:2303|Microbial Community Ecology and Physiology",
      "subfield": "ecology"
    }
  ],
  "title": "Rethinking the soil core microbiome",
  "title_text": "Rethinking the soil core microbiome",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T12:23:37Z",
  "url": "https://research.draconitic.com/paper/112xsg20nfc2c",
  "venue": "The New Phytologist",
  "versions": []
}